Hi Qi, thank you very much for you contribution. I will try to get your patch to the correct person during the upcoming Galaxy Conference. Cheers, Bjoern Am 13.06.2014 17:29, schrieb Qi, Chuyang:

Hi all,

When installing and testing the cd-hit tool from jjohnson from the main galaxy toolshed into my local instance of galaxy, I encountered a problem where galaxy cannot find the cd-hit program.

The error was: "/bin/sh: 1: cd-hit-est: not found"

As I debugged the problem, I found that there is an bug in the tool dependency. It installs the cd-hit programs but never moves the programs into the configurable galaxy install directory. This could cause many problems in the situation where users don't have cd-hit already installed on their computer and must depend on the tool dependency to run the tool.

I propose we add the following code to the tool dependency:

<action type="move_file"> <source>cd-hit</source> <destination>$INSTALL_DIR</destination> </action>

<action type="move_file"> <source>cd-hit-est</source> <destination>$INSTALL_DIR</destination> </action>

After I made these changes, I pushed the changes into a new repo on my local toolshed, I managed to successfully install cd-hit into a local and dev-test instance of galaxy and the cd-hit tool ran successfully.

Thanks for your understanding, Charles Qi

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